Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1240 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0222679274 sf0222673405 2 22679274 3.54E-32 8.53E-15
vg0222889740 sf0222883871 2 22889740 6.33E-32 4.01E-15
vg0818212763 sf0818210050 8 18212763 3.20E-23 3.45E-06
vg0906971590 sf0906970590 9 6971590 4.92E-23 NA
vg0500483303 sf0500483303 5 483303 5.97E-23 4.14E-06
vg0526059096 sf0525996516 5 26059096 8.23E-23 NA
vg0528277698 sf0528215053 5 28277698 5.85E-22 1.68E-06
vg0434773299 sf0434588190 4 34773299 9.41E-22 1.57E-09
vg1204550069 sf1204549057 12 4550069 6.98E-21 1.07E-06
vg0724353639 sf0724352645 7 24353639 8.05E-21 7.15E-08
vg0316148450 sf0316147097 3 16148450 7.21E-20 9.47E-07
vg0909362853 sf0909361852 9 9362853 1.57E-16 2.58E-06
vg0405832898 sf0405828337 4 5832898 2.32E-16 1.10E-07
vg1218624984 sf1218596420 12 18624984 2.84E-16 5.61E-07
vg0327037726 sf0327030779 3 27037726 NA 9.14E-09
vg0708623561 sf0708622566 7 8623561 NA 1.66E-07
vg0628766795 sf0628765797 6 28766795 NA 2.16E-07
vg0316512384 sf0316511029 3 16512384 NA 2.18E-07
vg0225225682 sf0225219813 2 25225682 NA 2.82E-07
vg0420266563 sf0420094608 4 20266563 NA 3.07E-07
vg0222982406 sf0222976537 2 22982406 NA 3.81E-07
vg0819584364 sf0819581651 8 19584364 NA 4.07E-07
vg0104901845 sf0104900845 1 4901845 NA 4.91E-07
vg0226545270 sf0226539401 2 26545270 NA 6.12E-07
vg0219344371 sf0219338503 2 19344371 NA 6.82E-07
vg0625536742 sf0625535745 6 25536742 NA 6.85E-07
vg0917346947 sf0917345946 9 17346947 NA 7.91E-07
vg0432666797 sf0432481686 4 32666797 NA 9.13E-07
vg0804649551 sf0804648554 8 4649551 NA 9.14E-07
vg0802090518 sf0802089521 8 2090518 NA 3.22E-06
vg0823456465 sf0823453752 8 23456465 NA 3.92E-06